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Wavelength-multiplexed Multi-mode EUV Reflection Ptychography based on Automatic-Differentiation

Published 24 Nov 2023 in eess.IV and physics.optics | (2311.14780v1)

Abstract: Ptychographic extreme ultraviolet (EUV) diffractive imaging has emerged as a promising candidate for the next-generation metrology solutions in the semiconductor industry, as it can image wafer samples in reflection geometry at the nanoscale. This technique has surged attention recently, owing to the significant progress in high-harmonic generation (HHG) EUV sources and advancements in both hardware and software for computation. In this study, a novel algorithm is introduced and tested, which enables wavelength-multiplexed reconstruction that enhances the measurement throughput and introduces data diversity, allowing the accurate characterisation of sample structures. To tackle the inherent instabilities of the HHG source, a modal approach was adopted, which represents the cross-density function of the illumination by a series of mutually incoherent and independent spatial modes. The proposed algorithm was implemented on a mainstream machine learning platform, which leverages automatic differentiation to manage the drastic growth in model complexity and expedites the computation using GPU acceleration. By optimising over 200 million parameters, we demonstrate the algorithm's capacity to accommodate experimental uncertainties and achieve a resolution approaching the diffraction limit in reflection geometry. The reconstruction of wafer samples with 20-nm heigh patterned gold structures on a silicon substrate highlights our ability to handle complex physical interrelations involving a multitude of parameters. These results establish ptychography as an efficient and accurate metrology tool.

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References (66)
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Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. 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In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. 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Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Porter, C.L., Tanksalvala, M., Gerrity, M., Miley, G., Zhang, X., Bevis, C., Shanblatt, E., Karl, R., Murnane, M.M., Adams, D.E., et al.: General-purpose, wide field-of-view reflection imaging with a tabletop 13 nm light source. Optica 4(12), 1552–1557 (2017) (8) Tanksalvala, M., Porter, C.L., Esashi, Y., Wang, B., Jenkins, N.W., Zhang, Z., Miley, G.P., Knobloch, J.L., McBennett, B., Horiguchi, N., et al.: Nondestructive, high-resolution, chemically specific 3d nanostructure characterization using phase-sensitive euv imaging reflectometry. Science Advances 7(5), 9667 (2021) (9) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tanksalvala, M., Porter, C.L., Esashi, Y., Wang, B., Jenkins, N.W., Zhang, Z., Miley, G.P., Knobloch, J.L., McBennett, B., Horiguchi, N., et al.: Nondestructive, high-resolution, chemically specific 3d nanostructure characterization using phase-sensitive euv imaging reflectometry. Science Advances 7(5), 9667 (2021) (9) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. 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Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. 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Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.D., Shanblatt, E.R., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: High contrast 3d imaging of surfaces near the wavelength limit using tabletop euv ptychography. Ultramicroscopy 158, 98–104 (2015) (7) Porter, C.L., Tanksalvala, M., Gerrity, M., Miley, G., Zhang, X., Bevis, C., Shanblatt, E., Karl, R., Murnane, M.M., Adams, D.E., et al.: General-purpose, wide field-of-view reflection imaging with a tabletop 13 nm light source. Optica 4(12), 1552–1557 (2017) (8) Tanksalvala, M., Porter, C.L., Esashi, Y., Wang, B., Jenkins, N.W., Zhang, Z., Miley, G.P., Knobloch, J.L., McBennett, B., Horiguchi, N., et al.: Nondestructive, high-resolution, chemically specific 3d nanostructure characterization using phase-sensitive euv imaging reflectometry. Science Advances 7(5), 9667 (2021) (9) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Porter, C.L., Tanksalvala, M., Gerrity, M., Miley, G., Zhang, X., Bevis, C., Shanblatt, E., Karl, R., Murnane, M.M., Adams, D.E., et al.: General-purpose, wide field-of-view reflection imaging with a tabletop 13 nm light source. Optica 4(12), 1552–1557 (2017) (8) Tanksalvala, M., Porter, C.L., Esashi, Y., Wang, B., Jenkins, N.W., Zhang, Z., Miley, G.P., Knobloch, J.L., McBennett, B., Horiguchi, N., et al.: Nondestructive, high-resolution, chemically specific 3d nanostructure characterization using phase-sensitive euv imaging reflectometry. Science Advances 7(5), 9667 (2021) (9) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tanksalvala, M., Porter, C.L., Esashi, Y., Wang, B., Jenkins, N.W., Zhang, Z., Miley, G.P., Knobloch, J.L., McBennett, B., Horiguchi, N., et al.: Nondestructive, high-resolution, chemically specific 3d nanostructure characterization using phase-sensitive euv imaging reflectometry. Science Advances 7(5), 9667 (2021) (9) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. 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In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Porter, C.L., Tanksalvala, M., Gerrity, M., Miley, G., Zhang, X., Bevis, C., Shanblatt, E., Karl, R., Murnane, M.M., Adams, D.E., et al.: General-purpose, wide field-of-view reflection imaging with a tabletop 13 nm light source. Optica 4(12), 1552–1557 (2017) (8) Tanksalvala, M., Porter, C.L., Esashi, Y., Wang, B., Jenkins, N.W., Zhang, Z., Miley, G.P., Knobloch, J.L., McBennett, B., Horiguchi, N., et al.: Nondestructive, high-resolution, chemically specific 3d nanostructure characterization using phase-sensitive euv imaging reflectometry. Science Advances 7(5), 9667 (2021) (9) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tanksalvala, M., Porter, C.L., Esashi, Y., Wang, B., Jenkins, N.W., Zhang, Z., Miley, G.P., Knobloch, J.L., McBennett, B., Horiguchi, N., et al.: Nondestructive, high-resolution, chemically specific 3d nanostructure characterization using phase-sensitive euv imaging reflectometry. Science Advances 7(5), 9667 (2021) (9) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. 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Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. 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Optics express 23(4), 4421–4434 (2015) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. 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Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. 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Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.D., Shanblatt, E.R., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: High contrast 3d imaging of surfaces near the wavelength limit using tabletop euv ptychography. Ultramicroscopy 158, 98–104 (2015) (7) Porter, C.L., Tanksalvala, M., Gerrity, M., Miley, G., Zhang, X., Bevis, C., Shanblatt, E., Karl, R., Murnane, M.M., Adams, D.E., et al.: General-purpose, wide field-of-view reflection imaging with a tabletop 13 nm light source. Optica 4(12), 1552–1557 (2017) (8) Tanksalvala, M., Porter, C.L., Esashi, Y., Wang, B., Jenkins, N.W., Zhang, Z., Miley, G.P., Knobloch, J.L., McBennett, B., Horiguchi, N., et al.: Nondestructive, high-resolution, chemically specific 3d nanostructure characterization using phase-sensitive euv imaging reflectometry. Science Advances 7(5), 9667 (2021) (9) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Porter, C.L., Tanksalvala, M., Gerrity, M., Miley, G., Zhang, X., Bevis, C., Shanblatt, E., Karl, R., Murnane, M.M., Adams, D.E., et al.: General-purpose, wide field-of-view reflection imaging with a tabletop 13 nm light source. Optica 4(12), 1552–1557 (2017) (8) Tanksalvala, M., Porter, C.L., Esashi, Y., Wang, B., Jenkins, N.W., Zhang, Z., Miley, G.P., Knobloch, J.L., McBennett, B., Horiguchi, N., et al.: Nondestructive, high-resolution, chemically specific 3d nanostructure characterization using phase-sensitive euv imaging reflectometry. Science Advances 7(5), 9667 (2021) (9) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tanksalvala, M., Porter, C.L., Esashi, Y., Wang, B., Jenkins, N.W., Zhang, Z., Miley, G.P., Knobloch, J.L., McBennett, B., Horiguchi, N., et al.: Nondestructive, high-resolution, chemically specific 3d nanostructure characterization using phase-sensitive euv imaging reflectometry. Science Advances 7(5), 9667 (2021) (9) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. 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Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. 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Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Porter, C.L., Tanksalvala, M., Gerrity, M., Miley, G., Zhang, X., Bevis, C., Shanblatt, E., Karl, R., Murnane, M.M., Adams, D.E., et al.: General-purpose, wide field-of-view reflection imaging with a tabletop 13 nm light source. Optica 4(12), 1552–1557 (2017) (8) Tanksalvala, M., Porter, C.L., Esashi, Y., Wang, B., Jenkins, N.W., Zhang, Z., Miley, G.P., Knobloch, J.L., McBennett, B., Horiguchi, N., et al.: Nondestructive, high-resolution, chemically specific 3d nanostructure characterization using phase-sensitive euv imaging reflectometry. Science Advances 7(5), 9667 (2021) (9) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tanksalvala, M., Porter, C.L., Esashi, Y., Wang, B., Jenkins, N.W., Zhang, Z., Miley, G.P., Knobloch, J.L., McBennett, B., Horiguchi, N., et al.: Nondestructive, high-resolution, chemically specific 3d nanostructure characterization using phase-sensitive euv imaging reflectometry. Science Advances 7(5), 9667 (2021) (9) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. 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Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. 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Optics express 23(4), 4421–4434 (2015) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. 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Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. 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Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tanksalvala, M., Porter, C.L., Esashi, Y., Wang, B., Jenkins, N.W., Zhang, Z., Miley, G.P., Knobloch, J.L., McBennett, B., Horiguchi, N., et al.: Nondestructive, high-resolution, chemically specific 3d nanostructure characterization using phase-sensitive euv imaging reflectometry. Science Advances 7(5), 9667 (2021) (9) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Gardner, D.F., Tanksalvala, M., Shanblatt, E.R., Zhang, X., Galloway, B.R., Porter, C.L., Karl Jr, R., Bevis, C., Adams, D.E., Kapteyn, H.C., et al.: Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source. Nature Photonics 11(4), 259–263 (2017) (10) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. 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Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. 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Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wang, B., Brooks, N.J., Johnsen, P.C., Jenkins, N.W., Esashi, Y., Binnie, I., Tanksalvala, M., Kapteyn, H.C., Murnane, M.M.: High-fidelity ptychographic imaging of highly periodic structures enabled by vortex high harmonic beams. arXiv preprint arXiv:2301.05563 (2023) (11) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goldberg, K.A., Benk, M.P., Wojdyla, A., Johnson, D.G., Donoghue, A.P.: New ways of looking at masks with the sharp euv microscope. In: Extreme Ultraviolet (EUV) Lithography VI, vol. 9422, pp. 404–414 (2015). SPIE (12) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. 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Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Benk, M.P., Goldberg, K.A., Wojdyla, A., Anderson, C.N., Salmassi, F., Naulleau, P.P., Kocsis, M.: Demonstration of 22-nm half pitch resolution on the sharp euv microscope. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena 33(6), 06–01 (2015) (13) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Rodenburg, J.M., Hurst, A., Cullis, A.G., Dobson, B.R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K., Johnson, I.: Hard-x-ray lensless imaging of extended objects. Physical review letters 98(3), 034801 (2007) (14) Thibault, P., Dierolf, M., Menzel, A., Bunk, O., David, C., Pfeiffer, F.: High-resolution scanning x-ray diffraction microscopy. Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. 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Science 321(5887), 379–382 (2008) (15) Loetgering, L., Witte, S., Rothhardt, J.: Advances in laboratory-scale ptychography using high harmonic sources. Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. 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Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. 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JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. 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Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. 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Optics Express 30(3), 4133–4164 (2022) (16) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. 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Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ditmire, T., Gumbrell, E., Smith, R., Tisch, J., Meyerhofer, D., Hutchinson, M.: Spatial coherence measurement of soft x-ray radiation produced by high order harmonic generation. Physical Review Letters 77(23), 4756 (1996) (17) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zerne, R., Altucci, C., Bellini, M., Gaarde, M.B., Hänsch, T., L’Huillier, A., Lyngå, C., Wahlström, C.-G.: Phase-locked high-order harmonic sources. Physical Review Letters 79(6), 1006 (1997) (18) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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(2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Bartels, R.A., Paul, A., Green, H., Kapteyn, H.C., Murnane, M.M., Backus, S., Christov, I.P., Liu, Y., Attwood, D., Jacobsen, C.: Generation of spatially coherent light at extreme ultraviolet wavelengths. Science 297(5580), 376–378 (2002) (19) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Guizar-Sicairos, M., Fienup, J.R.: Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Optics express 16(10), 7264–7278 (2008) (20) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. 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Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A.M., Rodenburg, J.M.: An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109(10), 1256–1262 (2009) (21) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Batey, D.J., Claus, D., Rodenburg, J.M.: Information multiplexing in ptychography. Ultramicroscopy 138, 13–21 (2014) (22) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, B., Gardner, D.F., Seaberg, M.H., Shanblatt, E.R., Porter, C.L., Karl, R., Mancuso, C.A., Kapteyn, H.C., Murnane, M.M., Adams, D.E.: Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb. Optics express 24(16), 18745–18754 (2016) (23) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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(2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Brooks, N.J., Wang, B., Binnie, I., Tanksalvala, M., Esashi, Y., Knobloch, J.L., Nguyen, Q.L., McBennett, B., Jenkins, N.W., Gui, G., et al.: Temporal and spectral multiplexing for euv multibeam ptychography with a high harmonic light source. Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. 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Optics Express 30(17), 30331–30346 (2022) (24) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. 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Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
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Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Liu, X., De Beurs, A.C., Du, M., Kuijper, G., Eikema, K.S., Witte, S.: Tailoring spatial entropy in extreme ultraviolet focused beams for multispectral ptychography. Optica 8(2), 130–138 (2021) (25) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Whitehead, L., Williams, G., Quiney, H., Vine, D., Dilanian, R., Flewett, S., Nugent, K., Peele, A.G., Balaur, E., McNulty, I.: Diffractive imaging using partially coherent x rays. Physical review letters 103(24), 243902 (2009) (26) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 23(4), 4421–4434 (2015) Thibault, P., Menzel, A.: Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71 (2013) (27) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Clark, J.N., Huang, X., Harder, R.J., Robinson, I.K.: Dynamic imaging using ptychography. Physical review letters 112(11), 113901 (2014) (28) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. 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Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Chen, Z., Odstrcil, M., Jiang, Y., Han, Y., Chiu, M.-H., Li, L.-J., Muller, D.A.: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose. Nature communications 11(1), 2994 (2020) (29) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Tschernajew, M., Hädrich, S., Klas, R., Gebhardt, M., Horsten, R., Weerdenburg, S., Pyatchenkov, S., Coene, W., Rothhardt, J., Eidam, T., et al.: High repetition rate high harmonic generation with ultra-high photon flux. In: Laser Applications Conference, pp. 2–21 (2020). Optica Publishing Group (30) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. 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Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. 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Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kirsche, A., Gebhardt, M., Klas, R., Eisenbach, L., Eschen, W., Buldt, J., Stark, H., Rothhardt, J., Limpert, J.: Continuously tunable high photon flux high harmonic source. Optics Express 31(2), 2744–2753 (2023) (31) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. Journal of Marchine Learning Research 18, 1–43 (2018) (32) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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(2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. 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Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
  31. Jurling, A.S., Fienup, J.R.: Applications of algorithmic differentiation to phase retrieval algorithms. JOSA A 31(7), 1348–1359 (2014) (33) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. 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Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
  32. Kandel, S., Maddali, S., Allain, M., Hruszkewycz, S.O., Jacobsen, C., Nashed, Y.S.: Using automatic differentiation as a general framework for ptychographic reconstruction. Optics express 27(13), 18653–18672 (2019) (34) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Bouchet, D., Loetgering, L., Mosk, A.P.: Efficient and flexible approach to ptychography using an optimization framework based on automatic differentiation. OSA Continuum 4(1), 121–128 (2021) (35) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
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Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. 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Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
  34. Kharitonov, K., Mehrjoo, M., Ruiz-Lopez, M., Keitel, B., Kreis, S., Seyrich, M., Pop, M., Plönjes, E.: Flexible ptychography platform to expand the potential of imaging at free electron lasers. Optics express 29(14), 22345–22365 (2021) (36) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maathuis, K., Seifert, J., Mosk, A.P.: Sensor fusion in ptychography. Optics Continuum 1(9), 1909–1917 (2022) (37) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Nashed, Y.S., Kandel, S., Gürsoy, D., Jacobsen, C.: Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science advances 6(13), 3700 (2020) (38) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Du, M., Kandel, S., Deng, J., Huang, X., Demortiere, A., Nguyen, T.T., Tucoulou, R., De Andrade, V., Jin, Q., Jacobsen, C.: Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation. Optics express 29(7), 10000–10035 (2021) (39) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. 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Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wolf, E.: New theory of partial coherence in the space–frequency domain. part i: spectra and cross spectra of steady-state sources. JOSA 72(3), 343–351 (1982) (40) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Lahiri, A.: Chapter 7 - optical coherence: Statistical optics. In: Lahiri, A. (ed.) Basic Optics, pp. 605–696. Elsevier, Amsterdam (41) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? 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Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. 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Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
  40. Odstrcil, M., Baksh, P., Boden, S., Card, R., Chad, J., Frey, J., Brocklesby, W.: Ptychographic coherent diffractive imaging with orthogonal probe relaxation. Optics express 24(8), 8360–8369 (2016) (42) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. 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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
  41. Thibault, P., Guizar-Sicairos, M.: Maximum-likelihood refinement for coherent diffractive imaging. New Journal of Physics 14(6), 063004 (2012) (43) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. 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Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
  42. Godard, P., Allain, M., Chamard, V., Rodenburg, J.: Noise models for low counting rate coherent diffraction imaging. Optics express 20(23), 25914–25934 (2012) (44) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Odstrčil, M., Menzel, A., Guizar-Sicairos, M.: Iterative least-squares solver for generalized maximum-likelihood ptychography. Optics express 26(3), 3108–3123 (2018) (45) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Seifert, J., Shao, Y., van Dam, R., Bouchet, D., van Leeuwen, T., Mosk, A.P.: Maximum-likelihood estimation in ptychography in the presence of poisson-gaussian noise statistics. arXiv preprint arXiv:2308.02436 (2023) (46) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014) (47) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Griewank, A., Walther, A.: Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation. SIAM, ??? (2008) (48) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. 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Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. 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Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Kakade, S.M., Lee, J.D.: Provably correct automatic sub-differentiation for qualified programs. Advances in neural information processing systems 31 (2018) (49) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
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Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. 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Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
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Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Matsushima, K.: Diffraction and Field Propagation, pp. 75–94. Springer, Cham (2020) (50) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Optics express 23(4), 4421–4434 (2015) Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
  49. Enders, B., Thibault, P.: A computational framework for ptychographic reconstructions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 472(2196), 20160640 (2016) (51) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E.H., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A., Guizar-Sicairos, M.: Ptychoshelves, a versatile high-level framework for high-performance analysis of ptychographic data. Journal of applied crystallography 53(2), 574–586 (2020) (52) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Flaes, D.B., Aidukas, T., Wechsler, F., Molina, D.S.P., Rose, M., Pelekanidis, A., Eschen, W., Hess, J.J., et al.: Ptylab. m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and fourier ptychography. Optics Express 31(9), 13763–13797 (2023) (53) Maiden, A., Johnson, D., Li, P.: Further improvements to the ptychographical iterative engine. Optica 4(7), 736–745 (2017) (54) Okuta, R., Unno, Y., Nishino, D., Hido, S., Loomis, C.: Cupy: A numpy-compatible library for nvidia gpu calculations. In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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In: Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS) (2017) (55) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Maiden, A., Humphry, M., Sarahan, M., Kraus, B., Rodenburg, J.: An annealing algorithm to correct positioning errors in ptychography. Ultramicroscopy 120, 64–72 (2012) (56) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
  55. Loetgering, L., Du, M., Eikema, K.S., Witte, S.: zpie: an autofocusing algorithm for ptychography. Optics letters 45(7), 2030–2033 (2020) (57) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Zhang, F., Peterson, I., Vila-Comamala, J., Diaz, A., Berenguer, F., Bean, R., Chen, B., Menzel, A., Robinson, I.K., Rodenburg, J.M.: Translation position determination in ptychographic coherent diffraction imaging. Optics express 21(11), 13592–13606 (2013) (58) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. 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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
  57. Dwivedi, P., Konijnenberg, A., Pereira, S., Urbach, H.: Lateral position correction in ptychography using the gradient of intensity patterns. Ultramicroscopy 192, 29–36 (2018) (59) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Ruan, T., Lv, W., Tao, Y., Zhang, J., Yan, X., Yang, D., Shi, Y.: Adaptive total variation based autofocusing strategy in ptychography. Optics and Lasers in Engineering 158, 107136 (2022) (60) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
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Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
  59. Van Heel, M., Keegstra, W., Schutter, W., Van Bruggen, E.: Arthropod hemocyanin structures studied by image analysis. Life Chem. Rep. Suppl 1(69-73), 5 (1982) (61) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
  60. Koho, S., Tortarolo, G., Castello, M., Deguchi, T., Diaspro, A., Vicidomini, G.: Fourier ring correlation simplifies image restoration in fluorescence microscopy. Nature communications 10(1), 3103 (2019) (62) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Henke, B.L., Gullikson, E.M., Davis, J.C.: X-ray interactions: photoabsorption, scattering, transmission, and reflection at e= 50-30,000 ev, z= 1-92. Atomic data and nuclear data tables 54(2), 181–342 (1993) (63) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Krizhevsky, A., Sutskever, I., Hinton, G.E.: Imagenet classification with deep convolutional neural networks. Communications of the ACM 60(6), 84–90 (2017) (64) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Radford, A., Narasimhan, K., Salimans, T., Sutskever, I., et al.: Improving language understanding by generative pre-training (2018) (65) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556 (2014) (66) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Devlin, J., Chang, M.-W., Lee, K., Toutanova, K.: Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018) (67) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015) Goh, S., Bastiaens, H., Vratzov, B., Huang, Q., Bijkerk, F., Boller, K.J.: Fabrication and characterization of free-standing, high-line-density transmission gratings for the vacuum uv to soft x-ray range. Optics express 23(4), 4421–4434 (2015)
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